meffil.extract.genotypes: Extract genotype data from PLINK .raw files for Illumina 450K...

View source: R/extract-genotypes.r

meffil.extract.genotypesR Documentation

Extract genotype data from PLINK .raw files for Illumina 450K SNPs

Description

Extract genotype data from PLINK .raw files for Illumina 450K SNPs

Usage

meffil.extract.genotypes(filenames, verbose = F)

Arguments

filenames

A vector of filenames of PLINK .raw files from which to extract genotype data.

Value

Matrix with rows corresponding to SNPs, columns to samples and values equal to 0, 1 or 2 corresponding to genotypes.

Examples

R> writeLines(meffil.snp.names("450k"), con="snp-names.txt")
shell> plink --bfile dataset --extract snp-names.txt --recodeA --out genotypes.raw --noweb
R> filenames <- "genotypes.raw"
R> genotypes <- meffil.extract.genotypes(filenames)


perishky/meffil documentation built on June 9, 2024, 5:59 p.m.